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coronavirus
Coronavirus, 2020. Modified from the original illustration by David S. Goodsell@RCSB PDB

The recent outbreak of the Novel Coronavirus disease (COVID-19) is a serious threat to people all over the world. In order to understand and develop an effective drug against this virus (Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2), structural work on the related proteins has already started and the resultant entries are accumulating in the PDB. PDBj provides a portal page for the COVID-19 related entries for our users. New entries will be added simultaneously with the public release from the wwPDB.

An explanation article covering one of the proteins of this virus is available on the "Molecules of the Month" page below:

The tab "All entries" contains all PDB IDs, in case you want to check all independent entries, including group depositions by the same authors. The "Repr. entries" tab contains only representative PDB entries with the highest resolution, excluding duplicate entries with 100% amino acid sequence identitiy, even if they contain a different ligand. Finally, the "Latest entries" tab contains the latest entries released this week.


Created: 2020-10-28 (last edited: more than 1 year ago)2022-09-02
8U3O
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BU of 8u3o by Molmil
SARS-CoV-2 Main Protease A173V in complex with CDD-1819
Descriptor: (2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide, ORF1a polyprotein
Authors:Nnabuife, C, Palzkill, T.
Deposit date:2023-09-08
Release date:2024-09-18
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:SARS-CoV-2 Main Protease A173V in complex with CDD-1819
To Be Published
8ZBQ
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BU of 8zbq by Molmil
Local map of Omicron Subvariant JN.1 RBD with ACE2
Descriptor: Angiotensin-converting enzyme 2, Spike protein S2'
Authors:Yan, R.H, Yang, H.N.
Deposit date:2024-04-27
Release date:2024-09-18
Last modified:2024-11-20
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants.
Nat Commun, 15, 2024
9ATO
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XBB.1.5 spike/Nanosota-3C complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-3C, ...
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2024-02-27
Release date:2024-09-18
Last modified:2025-04-02
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Structure-guided in vitro evolution of nanobodies targeting new viral variants.
Plos Pathog., 20, 2024
8WFH
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Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
Descriptor: D1 scFv, Spike protein S1
Authors:Terekhov, S.S, Mokrushina, Y.A, Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
Deposit date:2023-09-19
Release date:2024-09-25
Last modified:2024-11-27
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
To Be Published
8WFM
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Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
Descriptor: Spike protein S1, T11 scFv
Authors:Terekhov, S.S, Mokrushina, Y.A, Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
Deposit date:2023-09-19
Release date:2024-09-25
Last modified:2024-11-27
Method:X-RAY DIFFRACTION (2.99 Å)
Cite:Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
To Be Published
9DN4
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Crystal structure of a SARS-CoV-2 20-mer RNA in complex with FAB BL3-6S97N
Descriptor: CHLORIDE ION, FAB BL3-6S97N HEAVY CHAIN, FAB BL3-6S97N LIGHT CHAIN, ...
Authors:Lovell, S, Cooper, A, Battaile, K.P, Hegde, S, Wang, J.
Deposit date:2024-09-16
Release date:2024-09-25
Last modified:2025-07-02
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Mechanistic studies of small molecule ligands selective to RNA single G bulges.
Nucleic Acids Res., 53, 2025
8WKE
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Sulfate-bound SARS-CoV-2 Nsp9
Descriptor: Non-structural protein 9, SULFATE ION
Authors:Chen, P.J, Huang, H.Y, Hsiao, W.C, Huang, C.Y.
Deposit date:2023-09-27
Release date:2024-10-02
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Sulfate-bound SARS-CoV-2 Nsp9
To Be Published
8WSJ
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Crystal structure of SARS-Cov-2 main protease, pH=6.5
Descriptor: 3C-like proteinase nsp5
Authors:Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
Deposit date:2023-10-17
Release date:2024-10-02
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Crystal structure of SARS-Cov-2 main protease, pH=6.5
To Be Published
8WSK
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Crystal structure of SARS-Cov-2 main protease, pH=8.5
Descriptor: 3C-like proteinase nsp5
Authors:Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
Deposit date:2023-10-17
Release date:2024-10-02
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Crystal structure of SARS-Cov-2 main protease, pH=8.5
To Be Published
8K18
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Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
Descriptor: Spike protein S1, ZCP4C9 heavy chain, ZCP4C9 light chain
Authors:Bingjie, T, Shangyu, D.
Deposit date:2023-07-10
Release date:2024-10-09
Last modified:2025-06-25
Method:ELECTRON MICROSCOPY (3.68 Å)
Cite:Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
To Be Published
8K19
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Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
Descriptor: Spike protein S1, ZCP3B4 heavy chain, ZCP3B4 light chain
Authors:Tang, B, Dang, S.
Deposit date:2023-07-10
Release date:2024-10-09
Last modified:2025-06-25
Method:ELECTRON MICROSCOPY (3.88 Å)
Cite:Ultrapotent class I neutralizing antibodies post Omicron breakthrough infection overcome broad SARS-CoV-2 escape variants.
Ebiomedicine, 108, 2024
8WXL
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Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2023-10-30
Release date:2024-10-09
Last modified:2024-11-06
Method:ELECTRON MICROSCOPY (2.59 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUX
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Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-14
Release date:2024-10-09
Last modified:2025-06-18
Method:ELECTRON MICROSCOPY (3.22 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XV0
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Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-14
Release date:2024-10-09
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XVM
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Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-15
Release date:2024-10-09
Last modified:2024-10-23
Method:ELECTRON MICROSCOPY (2.77 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
9IU1
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BU of 9iu1 by Molmil
Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-07-20
Release date:2024-10-09
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (4.3 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8WPW
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BU of 8wpw by Molmil
Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CB6 fab mutant heavy chain, CB6 fab mutant light chain, ...
Authors:Su, C, Qi, J.X, Gao, G.F.
Deposit date:2023-10-10
Release date:2024-10-16
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.49 Å)
Cite:An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
8WPY
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BU of 8wpy by Molmil
Cryo-EM structure of SARS-CoV-2 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
Descriptor: CB6 fab mutant heavy chain, CB6 fab mutant light chain, S304 fab heavy chain, ...
Authors:Su, C, Qi, J.X, Gao, G.F.
Deposit date:2023-10-10
Release date:2024-10-16
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.02 Å)
Cite:An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
9ATM
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BU of 9atm by Molmil
SARS-CoV-2 EG.5 RBD bound to the VIR-7229 and the S2H97 Fab fragments
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2024-02-27
Release date:2024-10-16
Last modified:2024-12-25
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU1
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SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ...
Authors:Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D, Structural Genomics Consortium (SGC)
Deposit date:2024-02-27
Release date:2024-10-16
Last modified:2024-12-25
Method:X-RAY DIFFRACTION (2.41 Å)
Cite:A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU2
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VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Tortorici, M.A, Park, Y.J, Veelser, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2024-02-28
Release date:2024-10-16
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9CMN
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BU of 9cmn by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease drug resistant mutant (E166A, L167F)
Descriptor: 3C-like proteinase nsp5
Authors:Kovalevsky, A, Coates, L, Gerlits, O.
Deposit date:2024-07-15
Release date:2024-10-16
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2 Å)
Cite:Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors.
J.Med.Chem., 67, 2024
9GS4
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BU of 9gs4 by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571130
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-13
Release date:2024-10-16
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8S6M
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BU of 8s6m by Molmil
SARS-CoV-2 BQ.1.1 RBD bound to the S2V29 and the S2H97 Fab fragments
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Errico, J.M, Park, Y.J, Rietz, T, Czudnochowski, N, Nix, J.C, Cameroni, E, Corti, D, Snell, G, Marco, A.D, Pinto, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2024-02-28
Release date:2024-10-23
Last modified:2024-12-25
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
8VIA
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Protective effect of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, PVI.V5-4 heavy chain, ...
Authors:Bajic, G.
Deposit date:2024-01-03
Release date:2024-10-23
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination.
Cell Rep, 43, 2024

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